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Detailed information for vg0427290211:

Variant ID: vg0427290211 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27290211
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCTTCCTCCTCACCTTCATCTTCCCCTTCTCCGTCCCCTTCCACCTGCCCATCAGTCAATCTGGCCTATTATTACCTCATCAAACCCTAATCAACAG[G/A]
AGGCTACAACCTCAATTCAAGGTGTTAGCTAGGACGAGGTGATCGATCATCGTACTCACCATGAATTAGGCCCATGGCAAGTGGTTGCGGTGGCAGCTGC

Reverse complement sequence

GCAGCTGCCACCGCAACCACTTGCCATGGGCCTAATTCATGGTGAGTACGATGATCGATCACCTCGTCCTAGCTAACACCTTGAATTGAGGTTGTAGCCT[C/T]
CTGTTGATTAGGGTTTGATGAGGTAATAATAGGCCAGATTGACTGATGGGCAGGTGGAAGGGGACGGAGAAGGGGAAGATGAAGGTGAGGAGGAAGATGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.50% 28.90% 0.59% 0.00% NA
All Indica  2759 94.20% 5.50% 0.36% 0.00% NA
All Japonica  1512 22.20% 76.60% 1.19% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.90% 7.10% 1.01% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 93.20% 6.70% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 5.90% 0.38% 0.00% NA
Temperate Japonica  767 5.00% 94.40% 0.65% 0.00% NA
Tropical Japonica  504 46.00% 51.80% 2.18% 0.00% NA
Japonica Intermediate  241 27.40% 71.80% 0.83% 0.00% NA
VI/Aromatic  96 68.80% 31.20% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0427290211 G -> A LOC_Os04g46060.1 intron_variant ; MODIFIER silent_mutation Average:62.813; most accessible tissue: Callus, score: 76.165 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427290211 NA 9.53E-13 mr1641 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 1.80E-18 mr1653 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 4.56E-06 mr1653 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 8.10E-08 mr1659 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 5.44E-18 mr1767 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 1.09E-12 mr1853 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 1.28E-13 mr1909 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211 NA 2.43E-10 mr1921 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251